Evaluation of Genome Sequencing Quality in Selected Plant Species Using Expressed Sequence Tags

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Advances in plant genome sequencing

(2012) John P. Hamilton et al.   PLANT JOURNAL

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

OrthoInspector: comprehensive orthology analysis and visual exploration

(2011) Benjamin Linard et al.   BMC BIOINFORMATICS

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies

(2011) Liliana Florea et al.   PLoS One

The largest eukaryotic genome of them all?

(2010) JAUME PELLICER et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Genome assembly quality: Assessment and improvement using the neutral indel model

(2010) S. Meader et al.   GENOME RESEARCH

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Crop genome sequencing: lessons and rationales

(2010) Catherine Feuillet et al.   TRENDS IN PLANT SCIENCE

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

(2010) Rami A. Dalloul et al.   PLOS BIOLOGY

De novo sequencing of plant genomes using second-generation technologies

(2009) M. Imelfort et al.   BRIEFINGS IN BIOINFORMATICS

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Cheap third-generation sequencing

(2009) Nicole Rusk   NATURE METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

De Novo Next Generation Sequencing of Plant Genomes

(2009) Steve Rounsley et al.   Rice

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis †

(2008) Gerardo Turcatti et al.   NUCLEIC ACIDS RESEARCH

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Single-Molecule DNA Sequencing of a Viral Genome

(2008) T. D. Harris et al.   SCIENCE

Short read fragment assembly of bacterial genomes

(2007) M. J. Chaisson et al.   GENOME RESEARCH